BackgroundThe common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns.ResultsA total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species.ConclusionsThis is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

the rockpool shrimp Palaemon elegans is an ecologically important crustacean species within the european coastline fauna. in the present study, genetic diversity and population structure and connectivity were assessed by examining 21 polymorphic microsatellite loci at 13 sampling sites located along the natural distribution range. All localities showed similar levels of genetic variability. Significant deficits of heterozygosity were recorded, most likely due to the presence of null alleles. Genetic structure analyses revealed two clearly genetically distinct groups within P. elegans but without following any geographical or oceanographic basis. thus, our results provided nuclear evidence for the existence of a Mediterranean cryptic species within P. elegans, highlighting the need to revise its taxonomic status. Regarding P. elegans sensu stricto, population structuring was reported across the Atlantic-Mediterranean transition area, where the Almería-orán front restricts the gene flow between the Atlantic and the Mediterranean population. Moreover, while population connectivity was suggested between all Mediterranean localities, some substructure was found within the Atlantic group. Canary Islands exhibited a weak but significant genetic differentiation from all Atlantic mainland localities, consistent with the isolation-by-distance pattern detected throughout the Atlantic population. Overall, all these findings provided new insights into the population biology of P. elegans complex. The rockpool shrimp Palaemon elegans Rathke, 1837 is a crustacean decapod common in tidal rockpools, Zostera, Posidonia and Cymodocea sea grasses meadows and it also can be found in hypersaline lagoons and in slightly brackish water close to river mouths 1. This species is characterized by its capability to adapt to highly variable environments, as it can cope with a wide range of salinities, temperatures and oxygen conditions 2,3. Regarding to the native geographical distribution of P. elegans, it ranges from the eastern Atlantic Ocean (from Scotland and Norway to Mauritania, including the Azores, Madeira and Canary Islands) to the entire Mediterranean Sea and the Black Sea 4. Unintentional introductions resulted in this shrimp inhabiting the Caspian Sea and the Aral open

The rockpool shrimp Palaemon elegans is considered an important crustacean species within the European coastline fauna. This species is experiencing an ongoing geographical expansion beyond its native distribution range due to unintentional human introductions. A better knowledge of the genetic diversity, geographic structure and connectivity of its populations is necessary. In the present study, microsatellite loci were isolated using the Illumina MiSeq platform. The microsatellite-enriched library sequencing produced 3.9 million raw reads. Reads were processed and primer pairs were designed for microsatellite sequences amplification. Ninety-six microsatellite loci were preliminary screened in individuals from Atlantic and Mediterranean localities. From them, 21 loci exhibited reliable polymorphism and were thoroughly characterized in 30 individuals from a Cantabrian locality (Spain). No linkage disequilibrium between pairs of loci was detected. Number of alleles per locus ranged from 2 to 12. Observed and expected heterozygosities ranged from 0.033 to 0.833 and from 0.033 to 0.869 respectively. No significant departure from the Hardy-Weinberg equilibrium was detected in most of loci. This is the first time that microsatellite markers have been developed for P. elegans. This characterized microsatellite suite provides new suitable tools for further analyses, facilitating the understanding of population genetics both in natural and introduced populations.

The common littoral shrimp Palaemon serratus is an ecologically and economically important decapod crustacean. Understanding the spatial structure of its populations is crucial to implement effective management strategies. In this study, 17 polymorphic microsatellite nuclear markers were examined in 252 individuals to explore the genetic diversity and the population structure underlying the geographical distribution of this crustacean in European waters. Basic genetic descriptors, population genetic analyses based on FST, analysis of the molecular variance (AMOVA), Bayesian clustering and the Mantel test were performed. Genetic differentiation was significant among sampling sites. AMOVAs and Bayesian assignment tests showed genetic differentiation among localities from the Atlantic coast and those belonging to the area of the Strait of Gibraltar and the Mediterranean Sea. The Guadalquivir estuary was significantly different from the remaining localities. A biogeographical break was detected to the west of the Strait of Gibraltar, and evidence of isolation by distance was obtained. Localities on both sides of the English Channel showed genetic differentiation with the rest of the Atlantic sampling sites, indicating a biogeographical break in this area. These results will contribute towards the better understanding of the biology and ecology of this shrimp and management of the valuable fishery. Two priority areas were delimited: the Atlantic and the Gibraltar–Mediterranean. The Guadalquivir estuary, Anglesey and Calais should also be considered as different genetic stocks.

The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.